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cathteam:clegg [2010/10/04 11:21] – cleggcathteam:clegg [2010/11/22 11:34] (current) – clegg
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 +====== Dr. Andrew B. Clegg ======
 +
 +{{ :cathteam:sausage.jpg|Andrew with a half-metre sausage, found (and eaten) on holiday in Germany recently}}
 +===== Senior Research Associate, CATH Development =====
 +
 +A member of the [[cathteam:index|Orengo group]] since June 2008, I am the technical lead on the [[http://funcnet.eu/|FuncNet]] platform, which brings together an ensemble of protein function analysis tools from various groups around Europe. This work is supported by the EU-funded [[http://www.embracegrid.info/|EMBRACE]] and [[http://enfin.org.|ENFIN]] research networks.
 +
 +I'm involved in various other initiatives to extend the capabilities of [[http://cathdb.info/|CATH]] and [[http://gene3d.biochem.ucl.ac.uk/Gene3D/|Gene3D]] and enable them to interoperate better with bioinformatics resources at other organizations.
 +
 +I also write and maintain [[http://biotext.org.uk|biotext.org.uk]].
 +
 +Contact:
 +
 +{{:cathteam:ucl_email_3.png|}}
 +
 +http://twitter.com/andrew_clegg
 +
 +===== Academic Background =====
 +
 +I am a data scientist and software developer with experience in the fields of molecular biology, clinical research, public health and the pharmaceutical industry. 
 +
 +My MSc and PhD projects at [[http://www.cryst.bbk.ac.uk/|Birkbeck]] were on text mining techniques for bioinformatics, and this is a field I am still involved in. My {{:cathteam:clegg_thesis.pdf|thesis}}, supervised by [[http://people.cryst.bbk.ac.uk/~ubcg60a/group/index.html|Dr. Adrian Shepherd]], was on parsing sentences into phrase structure trees and dependency graphs, and extracting facts about gene regulation from these syntactic structures.
 +
 +As an undergrad I studied [[http://www.ucl.ac.uk/sts/|History and Philosophy of Science at UCL]] and I am still interested in the history and public perception of science, technology and medicine.
 +===== Current Research Interests =====
 +
 +As of Summer 2010, I'm mostly working on:
 +
 +  * Visualization of biological networks
 +  * Information retrieval and text mining
 +  * Integrative statistical methods for protein function prediction
 +  * Web service development (SOAP, REST, JSON-RPC)
 +  * Rich internet applications (AJAX, GWT)
 +
 +Outside of the lab, I'm the sole developer of the [[http://graphspider.sf.net/|GraphSpider/MPL]] natural-language processing toolkit, and also involved with [[http://smeshup.com/|Smesh]], a platform for analysis of social media data.
 +===== Publications =====
 +
 +Alison Cuff, Ian Sillitoe, Tony Lewis, Andrew Clegg, Robert Rentzsch, Nicholas Furnham, Marialuisa Pellegrini-Calace, David T. Jones, Janet Thornton and Christine A. Orengo, "[[http://nar.oxfordjournals.org/content/early/2010/11/19/nar.gkq1001.full|Extending CATH: Increasing Coverage of the Protein Structure Universe and Linking Structure with Function]]", in //Nucleic Acids Research// Database Issue **39** (2010).
 +
 +Juan A. G. Ranea, Ian Morilla, Jon G. Lees, Adam J. Reid, Corin Yeats, Andrew B. Clegg, Francisca Sánchez Jiménez and Christine Orengo, "[[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000945|Finding the 'Dark Matter' in Human and Yeast Protein Network Prediction and Modelling]]", in //PLoS Computational Biology// **6**:9 (2010).
 +
 +Contributor, //[[http://www.nice.org.uk/CG102|The management of bacterial meningitis and meningococcal septicaemia in children and young people younger than 16 years in primary and secondary care]]// (National Institute for Health and Clinical Excellence, 2010).
 +
 +Adam J. Reid, Juan A. G. Ranea, Andrew B. Clegg and Christine A. Orengo, "[[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010908|CODA: Accurate Detection of Functional Associations between Proteins in Eukaryotic Genomes Using Domain Fusion]]", in //PLoS ONE// **5**:6 (2010).
 +
 +Steve Pettifer, Jon Ison, Matus Kalas, Dave Thorne, Philip McDermott, Inge Jonassen, Ali Liaquat, Jose M. Fernandez, Jose M. Rodriguez, INB-Partners, David G. Pisano, Christophe Blanchet, Mahmut Uludag, Peter Rice, Edita Bartaseviciute, Kristoffer Rapacki, Maarten Hekkelman, Olivier Sand, Heinz Stockinger, Andrew B. Clegg, Erik Bongcam-Rudloff, Jean Salzemann, Vincent Breton, Teresa K. Attwood, Graham Cameron and Gert Vriend, "[[http://nar.oxfordjournals.org/cgi/content/full/gkq297?ijkey=0zo5SYmiVxwfNnc&keytype=ref|The EMBRACE Web Service Collection]]", in //Nucleic Acids Research// Web Servers Issue (2010).
 +
 +Corin Yeats, Jon Lees, Oliver Redfern, Andrew Clegg and Christine Orengo, "[[http://nar.oxfordjournals.org/cgi/content/full/gkp987|Gene3D: Merging Structure and Function For a Thousand Genomes]]", in //Nucleic Acids Research// Database Issue **38**:D296-D300 (2009).
 +
 +Pascal Kahlem, Andrew Clegg, Florian Reisinger, Ioannis Xenarios, Henning Hermjakob, Christine Orengo and Ewan Birney, "[[http://dx.doi.org/10.1016/j.crvi.2009.09.003|ENFIN -- A European network for integrative systems biology]]", in //Comptes Rendus Biologies// **332**:11 (2009).
 +
 +Contributor, //[[http://guidance.nice.org.uk/PH21|Reducing differences in the uptake of immunisations]]// (National Institute for Health and Clinical Excellence, 2009).
 +
 +Jose M. G. Izarzugaza, Anja Baresic, Lisa E. M. McMillan, Corin Yeats, Andrew B. Clegg, Christine A. Orengo, Andrew C. R. Martin and Alfonso Valencia, "[[http://www.biomedcentral.com/1471-2105/10/S8/S5|An integrated approach to the interpretation of Single Amino Acid Polymorphisms within the framework of CATH and Gene3D]]", in //BMC Bioinformatics// **10** (Suppl 8):S5 (2009).
 +
 +Renata Kabiljo, Andrew B. Clegg and Adrian J. Shepherd, "[[http://www.biomedcentral.com/1471-2105/10/233|A realistic assessment of methods for extracting gene/protein interactions from free text]]", in //BMC Bioinformatics// **10**:233 (2009).
 +
 +Andrew B. Clegg and Adrian J. Shepherd, "Syntactic pattern matching with GraphSpider and MPL", in //[[http://mars.cs.utu.fi/smbm2008/?q=proceedings|Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM'08)]]// (Turku, Finland: 2008).
 +
 +Andrew B. Clegg and Debbie Pledge, "Streamlining the clinical guideline production process with fuzzy citation matching", in //[[https://oa.doria.fi/handle/10024/41995|Proceedings of the First Conference on Text and Data Mining of Clinical Documents (Louhi'08)]]// (Turku, Finland: 2008).
 +
 +Andrew B. Clegg and Adrian J. Shepherd, "[[http://www.ncbi.nlm.nih.gov/pubmed/18712320|Text mining]]", in Jon Keith (ed.), //[[http://www.springerlink.com/content/g864wv1j02744r17/|Bioinformatics Volume II: Structure, Function and Applications]]// (Humana Press, New Jersey: 2008).
 +
 +Christian Guy, Emma Goddard, Emily Milner, Lisa Murch, and Andrew B. Clegg, "Looking into the core of the sun", in Hasok Chang and Catherine Jackson (eds.), //[[http://www.bshs.org.uk/bshs/publications/monograph_series/An_Element_of_Controversy|An Element of Controversy: The Life of Chlorine in Science, Medicine, Technology and War]]// (British Society for the History of Science: 2007).
 +
 +Andrew B. Clegg and Adrian J. Shepherd, "[[http://www.biomedcentral.com/1471-2105/8/24/|Benchmarking natural-language parsers for biological applications using dependency graphs]]", in //BMC Bioinformatics// **8**:24 (2007).
 +
 +Andrew B. Clegg and Adrian J. Shepherd, "[[http://www1.cs.columbia.edu/nlp/acl05soft/clegg.pdf|Evaluating and integrating treebank parsers on a biomedical corpus]]", in //Proceedings of the Association for Computational Linguistics Workshop on Software// (Ann Arbor, Michigan: 2005).
 +
 +===== Other Interests =====
 +
 +Along with [[http://www.cassj.co.uk/blog/|Cass Johnston]] and [[http://www3.imperial.ac.uk/theoreticalsystemsbiology/people/nathanharmston|Nathan Harmston]], I run an informal meet-up group for bioinformatics people and anyone else interested in the technical side of what we do: [[http://biogeeks.wordpress.com/|London BioGeeks]]. We have monthly-ish technical meetings (with talks) and social nights (with beer). Come along sometime. I'm also involved with the London [[http://www.meetup.com/Londonjavacommunity/|Java Community]] and [[http://groups.google.com/group/london-clojurians/?pli=1|Clojure Dojo]].
 +
 +I'm an occasional peer reviewer for [[http://bioinformatics.oupjournals.org/|Bioinformatics]] and the [[http://www.elsevier.com/locate/yjbin|Journal of Biomedical Informatics]], and I was on the programme committees for [[http://www.it.utu.fi/louhi/|Louhi 2008]], the [[http://compbio.uchsc.edu/BioNLP2009/|BioNLP 2009]] [[http://www-tsujii.is.s.u-tokyo.ac.jp/GENIA/SharedTask/|shared task]], and the [[http://www.acl2010.org/|ACL 2010]] track on "NLP for biology, medicine, law, etc."
 +
 +On a slightly less geeky note (or perhaps not) I am interested in electronica and avant-garde music, linguistics, London and cycling. Not usually at the same time, though. I also DJ occasionally at events like [[http://dronesclub.org.uk/|the Drones Club]] and write music reviews for websites such as [[http://connexionbizarre.net/|Connexion Bizarre]].
 +
 +===== Links =====
 +
 +My main site is at [[http://biotext.org.uk]]. My [[http://chomsky-ext.cryst.bbk.ac.uk/andrew|Birkbeck homepage]] still exists, for historical value only.
 +
 +===== Other CATH Team Members =====
 +
 +~~DIR?cols=page;description&hdrs=Person; Description~~

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